KrauthammerLab

University of Zurich & University Hospital Zurich

Our Research

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Clinical Data Science

Genome Data Science

Translational Bioinformatics

Speech & Cognition

Projects

BEDICT models

Predicting base editing efficiencies in both lab cells and living models

Systemic Sclerosis Subtype Analysis

Generative DL models patient trajectories

Alignment in Spoken Interaction

Studying how conversational coordination shapes meaning in human and machine communication

Data-driven psychiatry

Modeling speech and behavior to support mental health research and assessment

Modeling Spoken Language Beyond Text

Audio-first approaches to understanding language directly from speech

Protein Design

Generative AI for protein fitness optimization

MRIdle

Helping reduce idle time in the USZ Radiology department

Featured Publications

View All Publications

Zsolt Balazs, Panagiotis Balermpas, Ivna Ivankovic, Jonas Willmann, Todor Gitchev, Asher Bryant, Matthias Guckenberger, Michael Krauthammer, Nicolaus Andratschke

June 2024 Radiotherapy and Oncology

Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy

This study investigates the use of cfDNA sequencing to monitor tumor dynamics in patients undergoing high-dose radiotherapy, revealing correlations between genetic alterations and clinical outcomes.

DOI

Nicolas Mathis, Ahmed Allam, András Tálas, Lucas Kissling, Elena Benvenuto, Lukas Schmidheini, Ruben Schep, Tanav Damodharan, Zsolt Balázs, Sharan Janjuha, Eleonora I. Ioannidi, Desirée Böck, Bas van Steensel, Michael Krauthammer, Gerald Schwank

May 2024 Nature Biotechnology

Machine learning prediction of prime editing efficiency across diverse chromatin contexts

We developed machine learning models, PRIDICT2.0 and ePRIDICT, to predict prime editing efficiency, offering a robust tool for optimizing genome editing strategies across diverse chromatin contexts.

DOI

Alexandru Garaiman, Farhad Nooralahzadeh, Carina Mihai, Nicolas Perez, Nikitas Gkikopoulos, Mike Oliver Becker, Oliver Distler, Michael Krauthammer, Britta Maurer

December 2022 British Society for Rheumatology

Vision transformer assisting rheumatologists in screening for capillaroscopy changes in systemic sclerosis: an artificial intelligence model

The first objective of this study was to implement and assess the performance and reliability of a vision transformer (ViT)-based deep-learning model, an ‘off-the-shelf’ artificial intelligence solution, for identifying distinct signs of microangiopathy in nailfold capilloroscopy (NFC) images of patients with SSc. The second objective was to compare the ViT’s analysis performance with that of practising rheumatologists.

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Meet the Team

Principal Investigator

Michael Krauthammer

PI

Clinical Data Science, Translational Bioinformatics, Cancer Genetics

Senior Researchers and Postdocs

Zsolt Balázs

Senior Researcher

Bioinformatics, Cancer Genomics, Long-read sequencing, cfDNA sequencing

Ahmed Allam

Senior Researcher

Machine Learning

Lea Bogensperger

Postdoc

Machine Learning

Morteza Rohanian

Postdoc

Natural Language Processing, Clinical Machine Learning, Spoken Dialogue Processing

Farhad Nooralahzadeh

Senior Researcher

Natural Language Processing, Multimodal Multilingual Learning

Bowen Fan

Postdoc

clinical machine learning, manifold learning, graph learning

Nicolas Deperrois

NLP Engineer

Natural Language Processing, Computational Neuroscience

Ruijie Wang

Postdoctoral Researcher

Large Language Models, Natural Language Processing, Knowledge Graphs, Bioinformatics

Sonia Difrancesco

Postdoc

Digital Health, Chatbots & Wearable sensors, Machine Learning

Grad Students

Benjamin Gundersen

PhD Student

Science Fiction, Machine Learning, Programming

Beatrice Zanchi

Affiliated PhD Student

Electrical heart disease, Biomedical signal processing, Machine Learning, Time Series

Cécile Trottet

PhD Student

Machine Learning, Clinical Decision Support Systems

Lilith Feer

PhD Student

Machine Learning, Bioinformatics, Coding Best Practices, Personalized Medicine

Eline Meijer

Affiliated PhD Student

Clinical machine learning, Natural Language processing, Bioinformatics

Irene D'Onofrio

PhD Student

Multi-omics approaches, Machine Learning, Precision Medicine, Cancer biology

Manuela Merlo

PhD Student

Machine Learning, Reinforcement Learning, Large Language Models

Puck Quarles van Ufford

Visiting PhD Student

Prediction models for patient outcomes, Translation bioinformatics, Personalized medicine

Thibault Niederhauser

PhD Student

Machine Learning, Precision Medicine, Multi-Omics Integration, Neuro AI

Research Software Engineers

Todor Gitchev

Senior Research Software Engineer

Bioinformatics, Applied Mathematics, Genomics & Epigenetics, Algorithms

Mark McMahon

Senior Research Software Engineer

Data Science Tooling, Statistics, Machine Learning

Dhivyabharathi Ramasamy

Data Engineer

Research Assistants

Delia Haag

Master student

Machine Learning for Health Care, Biostatistics

Giulia Rathmes

Physician

Epidemiology, Biostatistics, Machine Learning for Health Care, Internal Medicine

Administrators

Claudia Stenger

Administrative Assistant

Oindrila Chakraborty

Project Manager

Project Management, Information Technology, Data Science

Affiliated Researchers

Manuel Schürch

Postdoc

Machine Learning, Gaussian Processes, Time Series

Ana Claudia Sima

Affiliated Senior Researcher

Knowledge Graphs, Semantic Search, Natural Language Processing, Bioinformatics

Diane Duroux

Affiliated Postdoc

Personalized medicine, Translational bioinformatics, Multimodal learning

Fabio Rinaldi

Research Group Leader

Jan Bartussek

Research Group Leader

Physiology and Pathophysiology, Nonlinear Dynamics, Mechanistic Modelling

Tilman Beck

Affiliated Researcher

Clinical NLP, Domain Adaptation, Deep Learning

Alumni

Ivna Ivanković

PhD Student

Amina Mollaysa

Postdoc

Kyriakos Schwarz

PhD Student

Nicolas Perez

Postdoc

Laura Kinkead

Senior Research Software Engineer

Nivitha Punniyamoorthy

BSc student

Matteo Berchier

Research Assistant

Matthias Dittberner

Data Scientist

Anna Sintsova

Postdoc

Aron Horvath

Postdoctoral Researcher

Chiara Rohrer

Master student

Daniel Eigensatz

Master student

Daniel Trejo Banos

Postdoctoral researcher

Elias Norri

Master student

Ernesto Sanchez Tejedor

Master student

Han Yuan

Visiting PhD Student

Jean Radig

Master student

Kürşat Birgin

Master student

Leopold Franz

Research Assistant

Lukas Bachmann

Physician

Maria Lambrinos

Master student

Matthias Joos

Associated Data Engineer, USZ

Melissa Ensmenger

MSc Student

Melissa Teoh

Master student

Mike Vollenweider

Master student

Noah Wolford

Master’s student

Richard Affolter

Master Thesis Student

Sanghwan Kim

Research Assistant

Sebastian

Mascot

Simon

Mascot

Siyuan Luo

MSc student

Timo Rieger

Master student

Wadusan Sebastianpillai

MSc student

Xiaocheng Yang

Master student

Xiaochen Zheng

PhD Student

Xingyu Chen

Research Assistant

Mascots

Globi

Senior Data Masseuse

Sleeping, Hunting birds and mice, Scratching trees

Iskra

Feel-good and Security Officer

Being the fastest dog in the neighborhood, Maintaining owner’s physical and mental health, Living the best day of her life every day

Oscar

The Last Airbender

Jumping all over the place 🦘, Knocking over Chess pieces ♟️♕, remote control 📺 and everything in front of him, Playing soccer ⚽ and chasing butterflies 🦋, Sleeping 😴 in front of laptops 💻, Participating in origami 📄🏮 and crafting activities 🧶🎨